Merge branch 'develop' into developtomchmmer

[jalview.git] / src / jalview / gui / Preferences.java

diff --git a/src/jalview/gui/Preferences.java b/src/jalview/gui/Preferences.java
index 9f9d6f8..a0a7511 100755 (executable)
--- a/src/jalview/gui/Preferences.java
+++ b/src/jalview/gui/Preferences.java
@@ -25,6 +25,8 @@ import jalview.bin.Cache;
 import jalview.gui.Help.HelpId;
 import jalview.gui.StructureViewer.ViewerType;
 import jalview.hmmer.HmmerCommand;
+import jalview.io.BackupFiles;
+import jalview.io.BackupFilesPresetEntry;
 import jalview.io.FileFormatI;
 import jalview.io.JalviewFileChooser;
 import jalview.io.JalviewFileView;
@@ -86,6 +88,15 @@ import ext.edu.ucsf.rbvi.strucviz2.StructureManager;
  */
 public class Preferences extends GPreferences
 {
+  // suggested list delimiter character
+  public static final String COMMA = ",";
+
+  public static final String HMMSEARCH_SEQCOUNT = "HMMSEARCH_SEQCOUNT";
+
+  public static final String HMMINFO_GLOBAL_BACKGROUND = "HMMINFO_GLOBAL_BACKGROUND";
+
+  public static final String HMMALIGN_TRIM_TERMINI = "HMMALIGN_TRIM_TERMINI";
+
   public static final String ENABLE_SPLIT_FRAME = "ENABLE_SPLIT_FRAME";
 
   public static final String SCALE_PROTEIN_TO_CDNA = "SCALE_PROTEIN_TO_CDNA";
@@ -112,8 +123,6 @@ public class Preferences extends GPreferences
 
   public static final String CYGWIN_PATH = "CYGWIN_PATH";
 
-  public static final String HMMSEARCH_DB_PATHS = "HMMSEARCH_DB_PATHS";
-
   public static final String HMMSEARCH_DBS = "HMMSEARCH_DBS";
 
   public static final String SORT_ANNOTATIONS = "SORT_ANNOTATIONS";
@@ -181,8 +190,6 @@ public class Preferences extends GPreferences
 
   JInternalFrame frame;
 
-  DasSourceBrowser dasSource;
-
   private WsPreferences wsPrefs;
 
   private OptionsParam promptEachTimeOpt = new OptionsParam(
@@ -203,8 +210,6 @@ public class Preferences extends GPreferences
     super();
     frame = new JInternalFrame();
     frame.setContentPane(this);
-    dasSource = new DasSourceBrowser();
-    dasTab.add(dasSource, BorderLayout.CENTER);
     wsPrefs = new WsPreferences();
     wsTab.add(wsPrefs, BorderLayout.CENTER);
     int width = 500, height = 450;
@@ -222,8 +227,8 @@ public class Preferences extends GPreferences
     /*
      * Set HMMER tab defaults
      */
-    hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
-    if (Cache.getDefault("USE_UNIPROT", false))
+    hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
+    if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
     {
       hmmerBackgroundUniprot.setSelected(true);
     }
@@ -232,7 +237,7 @@ public class Preferences extends GPreferences
       hmmerBackgroundAlignment.setSelected(true);
     }
     hmmerSequenceCount
-            .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+            .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
     hmmerPath.addActionListener(new ActionListener()
     {
@@ -250,23 +255,31 @@ public class Preferences extends GPreferences
         validateHmmerPath();
       }
     });
-    cygwinPath.setText(Cache.getProperty(CYGWIN_PATH));
-    cygwinPath.addActionListener(new ActionListener()
+    if (cygwinPath != null)
     {
-      @Override
-      public void actionPerformed(ActionEvent e)
+      String path = Cache.getProperty(CYGWIN_PATH);
+      if (path == null)
       {
-        validateCygwinPath();
+        path = FileUtils.getPathTo("bash");
       }
-    });
-    cygwinPath.addFocusListener(new FocusAdapter()
-    {
-      @Override
-      public void focusLost(FocusEvent e)
+      cygwinPath.setText(path);
+      cygwinPath.addActionListener(new ActionListener()
       {
-        validateCygwinPath();
-      }
-    });
+        @Override
+        public void actionPerformed(ActionEvent e)
+        {
+          validateCygwinPath();
+        }
+      });
+      cygwinPath.addFocusListener(new FocusAdapter()
+      {
+        @Override
+        public void focusLost(FocusEvent e)
+        {
+          validateCygwinPath();
+        }
+      });
+    }
 
     /*
      * Set Visual tab defaults
@@ -394,7 +407,7 @@ public class Preferences extends GPreferences
     gapLabel.setEnabled(!useLegacyGap.isSelected());
     gapColour.setEnabled(!useLegacyGap.isSelected());
     showHiddenAtStart
-            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, true));
+            .setSelected(Cache.getDefault(SHOW_OV_HIDDEN_AT_START, false));
 
     /*
      * Set Structure tab defaults.
@@ -615,6 +628,12 @@ public class Preferences extends GPreferences
 
     annotations_actionPerformed(null); // update the display of the annotation
                                        // settings
+    
+    
+    /*
+     * Set Backups tab defaults
+     */
+    loadLastSavedBackupsOptions();
   }
 
   /**
@@ -727,14 +746,17 @@ public class Preferences extends GPreferences
     /*
      * Save HMMER settings
      */
-    Cache.applicationProperties.setProperty("TRIM_TERMINI",
+    Cache.applicationProperties.setProperty(HMMALIGN_TRIM_TERMINI,
             Boolean.toString(hmmrTrimTermini.isSelected()));
-    Cache.applicationProperties.setProperty("USE_UNIPROT",
+    Cache.applicationProperties.setProperty(HMMINFO_GLOBAL_BACKGROUND,
             Boolean.toString(hmmerBackgroundUniprot.isSelected()));
-    Cache.applicationProperties.setProperty("SEQUENCES_TO_KEEP",
+    Cache.applicationProperties.setProperty(HMMSEARCH_SEQCOUNT,
             hmmerSequenceCount.getText());
     Cache.setOrRemove(HMMER_PATH, hmmerPath.getText());
-    Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
+    if (cygwinPath != null)
+    {
+      Cache.setOrRemove(CYGWIN_PATH, cygwinPath.getText());
+    }
     AlignFrame[] frames = Desktop.getAlignFrames();
     if (frames != null && frames.length > 0)
     {
@@ -744,8 +766,8 @@ public class Preferences extends GPreferences
       }
     }
     
-    hmmrTrimTermini.setSelected(Cache.getDefault("TRIM_TERMINI", false));
-    if (Cache.getDefault("USE_UNIPROT", false))
+    hmmrTrimTermini.setSelected(Cache.getDefault(HMMALIGN_TRIM_TERMINI, false));
+    if (Cache.getDefault(HMMINFO_GLOBAL_BACKGROUND, false))
     {
       hmmerBackgroundUniprot.setSelected(true);
     }
@@ -754,7 +776,7 @@ public class Preferences extends GPreferences
       hmmerBackgroundAlignment.setSelected(true);
     }
     hmmerSequenceCount
-            .setText(Cache.getProperty("SEQUENCES_TO_KEEP"));
+            .setText(Cache.getProperty(HMMSEARCH_SEQCOUNT));
     hmmerPath.setText(Cache.getProperty(HMMER_PATH));
 
     /*
@@ -899,8 +921,31 @@ public class Preferences extends GPreferences
     Cache.applicationProperties.setProperty("PAD_GAPS",
             Boolean.toString(padGaps.isSelected()));
 
-    dasSource.saveProperties(Cache.applicationProperties);
     wsPrefs.updateAndRefreshWsMenuConfig(false);
+
+    /*
+     * Save Backups settings
+     */
+    Cache.applicationProperties.setProperty(BackupFiles.ENABLED,
+            Boolean.toString(enableBackupFiles.isSelected()));
+    int preset = getComboIntStringKey(backupfilesPresetsCombo);
+    Cache.applicationProperties.setProperty(BackupFiles.NS + "_PRESET", Integer.toString(preset));
+
+    if (preset == BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM)
+    {
+      BackupFilesPresetEntry customBFPE = getBackupfilesCurrentEntry();
+      BackupFilesPresetEntry.backupfilesPresetEntriesValues.put(
+              BackupFilesPresetEntry.BACKUPFILESSCHEMECUSTOM, customBFPE);
+      Cache.applicationProperties
+              .setProperty(BackupFilesPresetEntry.CUSTOMCONFIG,
+                      customBFPE.toString());
+    }
+
+    BackupFilesPresetEntry savedBFPE = BackupFilesPresetEntry.backupfilesPresetEntriesValues
+            .get(preset);
+    Cache.applicationProperties.setProperty(
+            BackupFilesPresetEntry.SAVEDCONFIG, savedBFPE.toString());
+
     Cache.saveProperties();
     Desktop.instance.doConfigureStructurePrefs();
     try
@@ -1225,7 +1270,7 @@ public class Preferences extends GPreferences
   {
     useLegacyGap.setSelected(false);
     useLegacyGaps_actionPerformed(null);
-    showHiddenAtStart.setSelected(true);
+    showHiddenAtStart.setSelected(false);
     hiddenColour.setBackground(
             jalview.renderer.OverviewResColourFinder.OVERVIEW_DEFAULT_HIDDEN);
   }